Analyzing the Unborn Genome

Mapping the genome of a fetus from its mother’s blood could mean less risky screening for prenatal diseases.

A way of mapping the genome of an unborn child using DNA from the mother’s blood shows potential for broad genetic testing without risk to the fetus. While the technique is too expensive to be put into practice now, the research is important because it shows that the fetus’s entire genome is present in the mother’s blood.

“I think this paper is a major landmark to eventually offering noninvasive testing to all pregnant women,” says Arthur Beaudet, chairman of the department of molecular and human genetics at Baylor College of Medicine in Texas. Beaudet, who was not involved in the study, is pursuing similar research, to develop a method of isolating fetal cells from maternal blood.

The two most accurate prenatal tests for genetic abnormalities, such as Down syndrome, in use today are amniocentesis and chorionic villus sampling. Because these procedures are invasive and therefore carry a small risk of miscarriage, they are typically recommended only for women with known risk factors.

The discovery more than a decade ago of small amounts of free-floating fetal DNA circulating in maternal blood opened the possibility for noninvasive testing. A limited number of practical applications of this discovery are already in use. When a fetus is at risk for sex-linked diseases, some clinical labs analyze the free-floating DNA to determine the baby’s sex. It is also used to screen for Rh incompatibility syndrome, in which a blood-type mismatch between mother and fetus can trigger a dangerous immune reaction against the baby.

These two tests require analysis of only a single genetic factor. The broader analysis of the fetal DNA in maternal blood presents several challenges. For one thing, the DNA fragments are quite small—about 150 letters of DNA—making them difficult to piece together into a genome. For another, the fetal DNA accounts for only about 10 percent of the DNA fragments in blood, the remainder being the mother’s. That means scientists have to sequence the DNA about 60 times to sequence the fetal DNA six times. (It’s necessary to analyze the same stretch of DNA repeatedly in order to generate an accurate sequence.) The fact that the fetus shares half its DNA with its mother makes it especially difficult to determine which fragments are fetal and which are maternal.

“It’s like trying to assemble a jigsaw puzzle with millions of pieces, where 90 percent of the pieces are from another puzzle,” says Dennis Lo, a professor of chemical pathology at the Chinese University of Hong Kong, who first discovered fetal DNA in blood and is the lead author of the current study.

Thanks to rapidly falling costs in sequencing technology, it’s now possible to solve this large genetic puzzle. Using blood samples collected from a family in which both parents carry a single copy of a mutation linked to a blood disorder called beta-thalassemia, Lo and collaborators sequenced DNA from the mother’s blood and subsequently mapped the entire genome of the fetus.

To assemble the genome map, researchers analyzed both parents for common genetic variations to serve as genetic markers. They then searched the DNA for markers found only in the father’s genome, and used those to map the DNA the baby inherited from its father. Because the baby shares half its DNA with its mother, they adopted a quantitative approach to map maternal DNA. Sections of the genome that the fetus inherited from its mother would be overrepresented in the maternal blood, having both the maternal and fetal fragments. “Then we combined the maternal and paternal maps to create the fetal genetic map,” says Lo. Zeroing in on the region of interest, the researchers found that the fetus carried only one copy of the beta-thalassemia mutation, a result that was consistent with traditional testing.

Scientists had previously suspected that only portions of the fetus’s genome might be available for analysis, which would make it difficult to screen for diseases linked to aberrations scattered across the genome. But the new study, published Wednesday in Science Translational Medicine, demonstrates that the entire fetal genome can be found in the mother’s blood, offering the potential to expand testing to many more disorders.

Access to the entire genome would enable researchers to find not only single-letter mistakes in the DNA but also larger mistakes, such as deletions or duplications of whole segments of DNA, says Beaudet. These mistakes, which are being linked to a growing number of disorders, including mental retardation, autism, and schizophrenia, sometimes occur spontaneously in the development of eggs and sperm, and are therefore not present in parents.

Before clinical use can be made of the new finding, there are hurdles to overcome. In this case, researchers analyzed DNA they obtained via traditional invasive testing, taking a small piece of tissue from the placenta. The map they created with this DNA helped them to assemble the DNA that was derived non-invasively, much like the picture on a puzzle box aids in assembly of the puzzle. Given that the major reason to map a fetal genome would be to avoid invasive testing, this DNA obviously would not be available in clinical cases. Lo says there are ways around the problem; researchers could test DNA from other family members to aid the mapping process, for example.

However, that solution adds to the other major hurdle in the way of applying this technology: cost. Lo estimates the project cost $200,000 and took about six months. “You need sequencing equipment, bioinformaticians, and a huge amount of data storage—which is far more expensive” than existing methods, says Diana W. Bianchi, a researcher and physician at Tufts University School of Medicine, who was not involved in the study.

Lo says that the continued decrease in sequencing costs can be expected to resolve this problem in the next five years. He points to ways that costs might be reduced in the short term. Researchers could zero in on the DNA region of interest, rather than analyzing the entire genome, lowering both sequencing and data analysis costs. Additionally, the researchers found that fetal DNA fragments tended to be slightly shorter than the mother’s, providing a possible mechanism for selecting fetal DNA prior to sequencing, which would also cut down the amount of sequencing.

“I think the most urgent step is to try the targeted sequencing approach, which holds promise for being more practical, cheaper, and faster,” says Lo. His team is working on this now and aims to have results within the next five months.

The ability to analyze fetal DNA noninvasively is likely to intensify the debate about the ethics of preimplantation genetic testing, which involves analyzing embryos created from in vitro fertilization. Scientists, ethicists, physicians, and patients disagree about the types of conditions that should be tested for and how to deal with genetic information that indicates an unknown risk of inheriting a particular disease. “We are entering an era of fetal genomic medicine, and physicians need to get ready,” Bianchi says.